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| Status |
Public on Mar 13, 2024 |
| Title |
G7_rRNAdeplete_3 |
| Sample type |
SRA |
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| Source name |
C3H/10T1/2 (CCL-226) cells
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| Organism |
Mus musculus |
| Characteristics |
cell line: C3H/10T1/2 (CCL-226) cells
cell type: mesenchymal progenitor cells
genotype: Atrx knockout
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| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were harvested, washed with PBS, and flash frozen in liquid nitrogen. Cell pelet were sent to MSKCC integrated Genomics Operation for library prep.
Libraries were generated using NEBNext Ultra II kits.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
For the poly A RNAseq, transcript abundance was computed from FASTQ files using Salmon (v0.8.2) and the GENCODE reference transcript sequences, transcript counts were imported into R with the tximport R Bioconductor package, and differential gene expression was determined with the DESeq2 R Bioconductor package
For the rRNA depleted RNAseq, reads were aligned to the mm10 genome with STAR (v2.27.10a) setting the ‘—winAnchorMultimapNmax’ and ‘—outFilterMultimapNmax’ arguments to 100. Reads in repeats was then counted with the TElocal function from TEtranscripts and differential abundance calculated with DESeq2.
Assembly: mm10
Supplementary files format and content: Counts tables contain the raw counts quantified by Salmon and DESeq2 (ploy A) or TE transcripts (rRNA depleted).
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| Submission date |
Aug 03, 2023 |
| Last update date |
Mar 13, 2024 |
| Contact name |
Douglas Barrows |
| E-mail(s) |
dbarrows@rockefeller.edu
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| Phone |
7749940981
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| Organization name |
Rockefeller University
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| Street address |
1230 York Ave
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
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| Platform ID |
GPL19057 |
| Series (2) |
| GSE240027 |
ATRX guards against aberrant differentiation in mesenchymal progenitor cells (RNA-Seq) |
| GSE240030 |
ATRX guards against aberrant differentiation in mesenchymal progenitor cells |
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| Relations |
| BioSample |
SAMN36830667 |
| SRA |
SRX21242811 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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